I have been looking at the BES transportation tool, however as both BES's have their own SRP keys i am not sure its possible.

This is taken from the Tool manual.
"In an IBM Lotus Domino messaging environment, you must
configure the destination BlackBerry Enterprise Server instances to use the same SRP IDs that the source BlackBerry Enterprise
Server instances use." However is this just for Bulk Mode?

I am hoping that the BES transportation tool can just migrate users between the domains even if its phased over a few weeks.
Any help gratefully appreciated.

You've got a headache here, because you're currently running devices on two different databases. Maybe there was a reason for this originally... but when that second BES was added, you should have simply used the existing SQL database instead of making a second one. Then you could have easily moved all users to one BES and the transporter tool would have covered all the handhelds.

I think you're going to need to pick one BES (go with the smaller installation) and wipe/re-activate those handhelds on the new "consolidated" BES.
I don't know that you'll be able to use the transporter tool twice.

Yeah it is a bit odd having the two domains, it seems it was a bit of a mistake when the second server was set up.

Seems it may be possible to migrate though...

BlackBerry Enterprise Transporter modes
Live mode
"You can use live mode to move user accounts when the BlackBerry® Enterprise Server instances in both the destination BlackBerry
Domain and the source BlackBerry Domain are running. If you choose this mode, the BlackBerry Enterprise Server instances in
both BlackBerry Domain instances must use different SRP IDs.
In this mode, the BlackBerry Enterprise Server instances in the destination BlackBerry Domain must be running. This must occur
so that the BlackBerry Enterprise Transporter can monitor the organizer data synchronization and calendar synchronization
processes and IT administration commands (such as Resend IT Policy or Switch Service) that the destination BlackBerry Enterprise
Server instances send to the BlackBerry devices to complete the migration process."

So it seems I should be able to use the transportation tool with out the need for any additional SRP keys etc and free up a key post migration.

The phased approach (moving users over serveral weeks) from one BES DB to another should work. We did that from a 4.1.7 DB to a 5.0.2 DB (same as Nico57). We did it in batches of 20 users a day.

As you are dealing with older BES versions, you have to check with the transporter docs, if your versions are supported. I would move all users to the newer version of BES (you have to move more users, though).